--- a/scmap_scmap_cell.xml	Fri Nov 27 13:44:11 2020 +0000
+++ b/scmap_scmap_cell.xml	Tue Apr 23 07:48:26 2024 +0000
@@ -9,6 +9,8 @@
             -i '$index_single_cell_experiment' 
             -p '$project_single_cell_experiment' 
             --number-nearest-neighbours '$n_nearest_neighbours' 
+            --nearest-neighbours-threshold '$nearest_neighbours_threshold'
+            --threshold '$threshold'
             --cluster-col '${cluster_projection.cluster_col}' 
             --output-object-file '$output_single_cell_experiment' 
             --closest-cells-text-file '$closest_cells_text_file' 
@@ -21,6 +23,8 @@
       <param type="data" name="index_single_cell_experiment" label="Index SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features' and 'scmap index clusters', onto which another dataset will be projected." />
       <param type="data" name="project_single_cell_experiment" label="SingleCellExperiment object to project" format="rdata" help="File with serialized SingleCellExperiment object to project onto the index'" />
       <param name="n_nearest_neighbours" type="integer" label="Number of nearest neighbours" value='5' help="A positive integer specifying the number of nearest neighbours to find" />
+      <param name="nearest_neighbours_threshold" type="integer" label="Nearest neighbour threshold" value='3' help="A positive integer specifying the number of matching nearest neighbours required to label a cell." />
+      <param name="threshold" type="integer" label="Similarity threshold" value='0.7' help="Threshold on similarity (or probability for SVM and RF)." />
      <conditional name="cluster_projection">
         <param name="do_cluster_projection" type="boolean" checked="false" label="Annotate cells of the projection dataset using labels of the reference?" help="If cell cluster annotation is available for the reference datasets, in addition to finding top 10 nearest neighbours scmap-cell also allows to annotate cells of the projection dataset using labels of the reference."/>
         <when value="true" >
@@ -43,12 +47,29 @@
         <test>
             <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>
             <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
-            <param name="cluster_projection" value="true" />
+            <conditional name="cluster_projection">
+                <param name="do_cluster_projection" value="true" />
+                <param name="cluster_col" value="cell_type1" />
+            </conditional>
             <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/>
             <output name="closest_cells_clusters_csv" file="closest_cells_clusters.tsv" compare="sim_size" />
             <output name="closest_cells_text_file" file="closest_cells.tsv" compare="sim_size"/>
             <output name="closest_cells_similarities_text_file" file="closest_cells_similarities.tsv" compare="sim_size"/>
         </test>
+        <test>
+            <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>
+            <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
+            <conditional name="cluster_projection">
+                <param name="do_cluster_projection" value="true" />
+                <param name="cluster_col" value="cell_type1" />
+            </conditional>
+            <param name="nearest_neighbours_threshold" value="3" />
+            <param name="threshold" value="0.5" />
+            <output name="output_single_cell_experiment" file="closest_cells_clusters_copy.rds" compare="sim_size"/>
+            <output name="closest_cells_clusters_csv" file="closest_cells_clusters_copy.tsv" compare="sim_size" />
+            <output name="closest_cells_text_file" file="closest_cells_copy.tsv" compare="sim_size"/>
+            <output name="closest_cells_similarities_text_file" file="closest_cells_similarities_copy.tsv" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
     @HELP@